# Homology-modelling HEXA

## Contents

## Homology structure groups

We decided to choose every 5% one protein:

> 60% sequence identity | |||

PDB id | name | similarity | single template |

1ht6_A | AMY1, alpha-amylase iso | 95% | |

3aj7_A | Oligo-1,6-glucosidase | 90% | |

1h4p_A | Glucan 1,3-beta-glucosidase | 85.2% | |

3bc9_A | AMYB, alpha amylase, ca | 80.8% | X |

2zum_A | 458AA long hypothetical | 75% | |

3bmv_A | Cyclomaltodextrin gluca | 70.3% | |

2f2h_A | Putative family 31 gluc | 64.8% | |

3emz_A | Xylanase, endo-1,4-beta | 61% | |

> 40% | |||

2dep_A | Xylanase B, thermostabl | 54.9% | |

3cui_A | EXO-beta-1,4-glucanase; | 49.5% | X |

1vhc_A | Putative KHG/KDPG aldol | 45.1% | |

2hk0_A | D-psicose 3-epimerase | 40.8% | |

< 40% | |||

2g0w_A | LMO2234 protein; putati | 35.5% | |

3q94_A | Fructose-bisphosphate a | 30.0% | |

3hn3_A | Beta-G1, beta-glucuroni | 25.1% | |

3lut_A | Voltage-gated potassium | 20.1% | X |

## Calculation of the models

### Swissmodel

To calculate the models with Swiss-Model we used the [Webserver]. For the template with high sequence identity, we used the automated and the alignment method, for the other two templates we only used the alignment method.

The used alignments can be found [here].

### Modeller

We used Modeller from the command line. Therefore we followed the instructions, described [here].

First of all, we created an alignment for each of our three selected sequences. In the next step we used Modeller to model the 3D structure of the protein.

For Modeller we used the Pir Alignment format, which can be found here: [3BC9], [3CUI], [3LUT]

### iTasser

To calculate our models with iTasser we used the [Webserver]. We defined the target and template sequence, but this time without an alignment. We used the same template sequences as before.

## Results

### Swissmodel

3BC9:

todo

3CUI:

The detailed prediction can be found [here]

Swiss-Model also give same scores to give the user the possibility to estimate the quality of the predicted model, which are showed in the next paragraphes.

The most important score in the following table is the QMEAN4 score, because this score consists of the scores above and give the user the possibility to compare different results.

Global Score | ||

Scoring function term | Raw score | Z score |

C_beta interaction energy | 202.24 | -4.65 |

All-atom pairwise energy | 9942.28 | -6.16 |

Solvation energy | 67.79 | -8.08 |

Torsion angle energy | 76.36 | -7.72 |

QMEAN4 score | 0.057 | -11.76 |

Swiss-Modeler also returns some pictures, which show the qualitity of the model.

Predicted Structure:

Model qualitity:

3HN3:

The detailed prediction can be found [here]

Swiss-Model also give same scores to give the user the possibility to estimate the quality of the predicted model, which are showed in the next paragraphes.

The most important score in the following table is the QMEAN4 score, because this score consists of the scores above and give the user the possibility to compare different results.

Global Score | ||

Scoring function term | Raw score | Z score |

C_beta interaction energy | 120.70 | -5.31 |

All-atom pairwise energy | 2585.98 | -5.22 |

Solvation energy | 71.87 | -9.92 |

Torsion angle energy | 80.43 | -8.44 |

QMEAN4 score | 0.010 | -12.80 |

Swiss-Modeler also returns some pictures, which show the qualitity of the model.

Predicted Structure:

Model qualitity:

### Modeller

3BC9:

Modeller calculated one model for 3BC9, which can be seen in the next picture:

3CUI:

Modeller calculated one model for 3CUI, which can be seen in the next picture:

3HN3:

TODO Dienstag

### iTasser

## Analysis

### RMSD

To get the possibility to estimate the quality of the predicted models, we calculated the RMSD between the observed protein and the predicted protein. For this purpose, we used PyMol, because PyMol is able to superpose two 3D protein structures and to calculate the RMSD.

Therefore, we used following command:

align model1, model2

As an output, we got the superposed structures, the number of aligned residues and the RMSD.

We decided not to use the RMSD, which is calculated by Modeller, because we wanted to calculate the RMSD for each structure in the same way, to get comparative results.

** Results for 3BC9:**

Swissmodel | Modeller | iTasser | 3D-Jigsaw | ||||

Model 1 | Model 2 | Model 3 | Model 4 | Model 5 |